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This is the best way to merge. You will be making an entirely new layer that consists of all of the other layers that are visible.

You can merge all visible layers onto an existing layer, but you will then lose the solidarity of that particular layer. Instead, you should create a new layer, which will be blank and transparent by default.

With this new layer selected, and preferably on top of the stack (I’ll tell you why in a second), hold down the option (alt key for PC users), while selecting Merge Visible. This copies all the other layers and merges their information onto the new layer.

This layer should most often be on the top of the stack, especially if there are adjustment layers. This is because all visible layers, including adjustment layers are merged into the new layer without being lost. If you make this new, merged layer and it wasn’t above the adjustment layers, but rather resides below them, it will be receiving those adjustments twice!

Once because the adjustments are now part of the new layer, and twice because they are under the adjustment layers still!

With this new merged layer you are able to make adjustments to the all of the merged layers at once, or copy the layer and have the benefit of copying all layers together without flattening.